Chris Sander

Chris Sander

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Protein Structure Prediction Assisted with Sparse NMR Data in CASP13.

Proteins 2019 Oct 11. Epub 2019 Oct 11.

Center for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.

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http://dx.doi.org/10.1002/prot.25837DOI Listing
October 2019

Combining Evolutionary Covariance and NMR Data for Protein Structure Determination.

Methods Enzymol 2019 23;614:363-392. Epub 2018 Dec 23.

Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, United States; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, United States; Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, United States. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2018.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6640129PMC
August 2019

A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data.

Adv Exp Med Biol 2018;1105:153-169

Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.

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http://dx.doi.org/10.1007/978-981-13-2200-6_10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630173PMC
July 2019

Inferring protein 3D structure from deep mutation scans.

Nat Genet 2019 Jul 17;51(7):1170-1176. Epub 2019 Jun 17.

Department of Systems Biology, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41588-019-0432-9DOI Listing
July 2019

LLGL2 rescues nutrient stress by promoting leucine uptake in ER breast cancer.

Nature 2019 May 17;569(7755):275-279. Epub 2019 Apr 17.

Department of Medicine, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.

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http://www.nature.com/articles/s41586-019-1126-2
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http://dx.doi.org/10.1038/s41586-019-1126-2DOI Listing
May 2019

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Cancer Cell 2018 08 2;34(2):211-224.e6. Epub 2018 Aug 2.

ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; ETH Zurich, Department of Biology, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.07.001DOI Listing
August 2018

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer.

NPJ Syst Biol Appl 2018 2;4:26. Epub 2018 Jul 2.

1Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Auguste Piccard Hof 1, Zürich, Switzerland.

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http://dx.doi.org/10.1038/s41540-018-0064-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026592PMC
July 2018

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

Nat Genet 2018 05 16;50(5):682-692. Epub 2018 Apr 16.

The Institute of Cancer Research, London, UK.

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http://www.nature.com/articles/s41588-018-0086-z
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http://dx.doi.org/10.1038/s41588-018-0086-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372064PMC
May 2018

A Landscape of Metabolic Variation across Tumor Types.

Cell Syst 2018 Mar 27;6(3):301-313.e3. Epub 2018 Jan 27.

cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.12.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5876114PMC
March 2018

Mutation effects predicted from sequence co-variation.

Nat Biotechnol 2017 02 16;35(2):128-135. Epub 2017 Jan 16.

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383098PMC
February 2017

Mitochondrial respiratory gene expression is suppressed in many cancers.

Elife 2017 01 18;6. Epub 2017 Jan 18.

Department of Cell Biology, Harvard Medical School, Boston, United States.

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http://dx.doi.org/10.7554/eLife.21592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243113PMC
January 2017

Integrin-α10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma.

Cancer Discov 2016 10 30;6(10):1148-1165. Epub 2016 Aug 30.

Sarcoma Biology Laboratory, Sarcoma Disease Management Program, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Surgery, Weill Cornell Medical College, New York, New York.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5050162PMC
http://dx.doi.org/10.1158/2159-8290.CD-15-1481DOI Listing
October 2016

Structured States of Disordered Proteins from Genomic Sequences.

Cell 2016 Sep;167(1):158-170.e12

Department of Systems Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451116PMC
September 2016

3D RNA and Functional Interactions from Evolutionary Couplings.

Cell 2016 May 14;165(4):963-75. Epub 2016 Apr 14.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.03.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024353PMC
May 2016

rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R.

Bioinformatics 2016 04 3;32(8):1272-4. Epub 2015 Dec 3.

Developmental Therapeutic Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907377PMC
April 2016

PaxtoolsR: pathway analysis in R using Pathway Commons.

Bioinformatics 2016 04 18;32(8):1262-4. Epub 2015 Dec 18.

Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824129PMC
April 2016

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.

Cell Rep 2016 Mar 3;14(10):2476-89. Epub 2016 Mar 3.

Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794376PMC
March 2016

Mitochondrial DNA copy number variation across human cancers.

Elife 2016 Feb 22;5. Epub 2016 Feb 22.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.

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http://dx.doi.org/10.7554/eLife.10769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775221PMC
February 2016

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.

PLoS Comput Biol 2016 Feb 29;12(2):e1004765. Epub 2016 Feb 29.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771175PMC
February 2016

Spatial normalization of reverse phase protein array data.

PLoS One 2014 12;9(12):e97213. Epub 2014 Dec 12.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097213PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264691PMC
January 2016

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer.

Nucleic Acids Res 2016 Jan 20;44(D1):D986-91. Epub 2015 Nov 20.

Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK

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http://dx.doi.org/10.1093/nar/gkv1132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702822PMC
January 2016

Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis.

Neuro Oncol 2015 Oct 3;17(10):1356-64. Epub 2015 Mar 3.

Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.).

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http://dx.doi.org/10.1093/neuonc/nov027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578578PMC
October 2015

Applications of targeted proteomics in systems biology and translational medicine.

Proteomics 2015 Sep 16;15(18):3193-208. Epub 2015 Jul 16.

Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.

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http://dx.doi.org/10.1002/pmic.201500004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758406PMC
September 2015

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains.

Cell Syst 2015 Sep 23;1(3):197-209. Epub 2015 Sep 23.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2015.08.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982675PMC
September 2015

Protein structure determination by combining sparse NMR data with evolutionary couplings.

Nat Methods 2015 Aug 29;12(8):751-4. Epub 2015 Jun 29.

1] Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA. [2] Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA. [3] Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.

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http://dx.doi.org/10.1038/nmeth.3455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521990PMC
August 2015

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.

PLoS Comput Biol 2015 Jul 30;11(7):e1004182. Epub 2015 Jul 30.

Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.

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https://dash.harvard.edu/bitstream/handle/1/21462137/4520494
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http://dx.plos.org/10.1371/journal.pcbi.1004182
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http://dx.doi.org/10.1371/journal.pcbi.1004182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520494PMC
July 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Extensive decoupling of metabolic genes in cancer.

PLoS Comput Biol 2015 May 11;11(5):e1004176. Epub 2015 May 11.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1004176
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http://dx.doi.org/10.1371/journal.pcbi.1004176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427321PMC
May 2015

Alterations of DNA repair genes in the NCI-60 cell lines and their predictive value for anticancer drug activity.

DNA Repair (Amst) 2015 Apr 11;28:107-15. Epub 2015 Feb 11.

Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15687864150002
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http://dx.doi.org/10.1016/j.dnarep.2015.01.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385398PMC
April 2015

Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.

Science 2015 Apr 12;348(6230):124-8. Epub 2015 Mar 12.

Weill Cornell Medical College, New York, NY, 10065, USA. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

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http://dx.doi.org/10.1126/science.aaa1348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4993154PMC
April 2015

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Proc Natl Acad Sci U S A 2015 Apr 9;112(17):5413-8. Epub 2015 Apr 9.

Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden

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http://dx.doi.org/10.1073/pnas.1419956112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418893PMC
April 2015

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.

Genome Biol 2015 Feb 26;16:45. Epub 2015 Feb 26.

Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA.

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http://genomebiology.com/2015/16/1/45
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http://dx.doi.org/10.1186/s13059-015-0612-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381444PMC
February 2015

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.

Nature 2015 Jan 22;517(7533):205-8. Epub 2014 Oct 22.

1] Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA [2] Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA [3] Immunology Program, Sloan-Kettering Institute, New York, New York 10065, USA.

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http://dx.doi.org/10.1038/nature13828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354891PMC
January 2015

Identifying actionable targets through integrative analyses of GEM model and human prostate cancer genomic profiling.

Mol Cancer Ther 2015 Jan 7;14(1):278-88. Epub 2014 Nov 7.

Human Oncology and Pathogenesis Oncology Program, Memorial Sloan-Kettering Cancer Center, New York, New York. Department of Surgery and Division of Urology, Memorial Sloan-Kettering Cancer Center, New York, New York.

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http://mct.aacrjournals.org/content/14/1/278.full.pdf
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http://mct.aacrjournals.org/cgi/doi/10.1158/1535-7163.MCT-14
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http://dx.doi.org/10.1158/1535-7163.MCT-14-0542-TDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297258PMC
January 2015

Genome-wide analysis of noncoding regulatory mutations in cancer.

Nat Genet 2014 Nov 28;46(11):1160-5. Epub 2014 Sep 28.

1] Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217527PMC
November 2014

PconsFold: improved contact predictions improve protein models.

Bioinformatics 2014 Sep;30(17):i482-8

Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden, Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland and Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden, Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland and Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147911PMC
September 2014

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota.

PLoS Comput Biol 2013 12;9(12):e1003388. Epub 2013 Dec 12.

Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861043PMC
August 2014

Integrating biological pathways and genomic profiles with ChiBE 2.

BMC Genomics 2014 Aug 3;15:642. Epub 2014 Aug 3.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10065, USA.

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http://dx.doi.org/10.1186/1471-2164-15-642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131037PMC
August 2014

Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification.

PLoS One 2013 12;8(11):e80306. Epub 2013 Nov 12.

Department of Medical Biochemistry & Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080306PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827191PMC
July 2014

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.

Bioinformatics 2014 Jul 24;30(14):2051-9. Epub 2014 Mar 24.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 and Tri-Institutional Training Program in Computational Biology & Medicine, New York, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080742PMC
July 2014

PredictProtein--an open resource for online prediction of protein structural and functional features.

Nucleic Acids Res 2014 Jul 5;42(Web Server issue):W337-43. Epub 2014 May 5.

Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany Biosof LLC, New York, NY 10001, USA New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel Department of Biochemistry and Molecular Biophysics & New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA Institute for Advanced Study (TUM-IAS), Garching/Munich 85748, Germany.

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http://dx.doi.org/10.1093/nar/gku366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086098PMC
July 2014

Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy.

J Exp Med 2014 Jun 9;211(7):1379-91. Epub 2014 Jun 9.

Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065

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http://dx.doi.org/10.1084/jem.20132120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076578PMC
June 2014

Using biological pathway data with paxtools.

PLoS Comput Biol 2013 19;9(9):e1003194. Epub 2013 Sep 19.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1003194
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http://dx.doi.org/10.1371/journal.pcbi.1003194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777916PMC
April 2014

Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy.

Clin Cancer Res 2014 Apr 12;20(7):1955-64. Epub 2014 Mar 12.

Authors' Affiliations: Departments of Medicine, Surgery, Pathology, Radiology, and Computational Biology; Human Oncology and Pathogenesis Program; Genomics Core Laboratory, Memorial Sloan-Kettering Cancer Center; and Department of Medicine, Weill Medical College of Cornell University, New York, New York.

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http://dx.doi.org/10.1158/1078-0432.CCR-13-2345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140619PMC
April 2014

Collection, integration and analysis of cancer genomic profiles: from data to insight.

Curr Opin Genet Dev 2014 Feb 27;24:92-8. Epub 2014 Feb 27.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, Box 460, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2013.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084973PMC
February 2014

Evaluating cell lines as tumour models by comparison of genomic profiles.

Nat Commun 2013 ;4:2126

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, New York 10065, USA.

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http://dx.doi.org/10.1038/ncomms3126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715866PMC
January 2014

Pattern search in BioPAX models.

Bioinformatics 2014 Jan 16;30(1):139-40. Epub 2013 Sep 16.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866551PMC
January 2014

An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma.

J Natl Cancer Inst 2013 Dec 27;105(24):1862-70. Epub 2013 Nov 27.

Affiliations of authors: Urology Service, Department of Surgery (AAH, NM, BF, PHK, PR), Human Oncology & Pathogenesis Program (AAH, JJH); Epidemiology and Biostatistics (HF, ECZ), Computational Biology (AJ, NS, GC, CS), Genitourinary Oncology (MHV, RJM, JJH), and Department of Pathology (VER), Memorial Sloan-Kettering Cancer Center, New York, NY; USC Epigenome Center, University of Southern California, Los Angeles, California (HS, PWL); Weill Medical College, Cornell University, New York, NY (RJM, JJH, PR).

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http://dx.doi.org/10.1093/jnci/djt310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866155PMC
December 2013

SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer.

Cancer Cell 2013 Dec;24(6):738-50

Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2013.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910168PMC
December 2013

Analysis of microRNA-target interactions across diverse cancer types.

Nat Struct Mol Biol 2013 Nov 6;20(11):1325-32. Epub 2013 Oct 6.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nsmb.2678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982325PMC
November 2013

The BioPAX Validator.

Bioinformatics 2013 Oct 5;29(20):2659-60. Epub 2013 Aug 5.

The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789551PMC
October 2013

The Cancer Genome Atlas Pan-Cancer analysis project.

Nat Genet 2013 Oct;45(10):1113-20

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/ng.2764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919969PMC
October 2013

Emerging landscape of oncogenic signatures across human cancers.

Nat Genet 2013 Oct;45(10):1127-33

Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.2762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320046PMC
October 2013

The molecular diversity of Luminal A breast tumors.

Breast Cancer Res Treat 2013 Oct 6;141(3):409-20. Epub 2013 Oct 6.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA,

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http://dx.doi.org/10.1007/s10549-013-2699-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824397PMC
October 2013

The somatic genomic landscape of glioblastoma.

Cell 2013 Oct;155(2):462-77

Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA. Electronic address:

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https://www.genome.gov/Multimedia/Slides/TCGA2/27_Verhaak.pd
Web Search
http://linkinghub.elsevier.com/retrieve/pii/S009286741301208
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http://dx.doi.org/10.1016/j.cell.2013.09.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500PMC
October 2013

PiHelper: an open source framework for drug-target and antibody-target data.

Bioinformatics 2013 Aug 12;29(16):2071-2. Epub 2013 Jun 12.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722529PMC
August 2013

Pattern discovery and cancer gene identification in integrated cancer genomic data.

Proc Natl Acad Sci U S A 2013 Mar 21;110(11):4245-50. Epub 2013 Feb 21.

Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

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http://www.pnas.org/content/110/11/4245.full.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.1208949110
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http://dx.doi.org/10.1073/pnas.1208949110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600490PMC
March 2013

Using MEMo to discover mutual exclusivity modules in cancer.

Curr Protoc Bioinformatics 2013 Mar;Chapter 8:Unit 8.17

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1002/0471250953.bi0817s41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5563973PMC
March 2013

Protein structure prediction from sequence variation.

Nat Biotechnol 2012 Nov;30(11):1072-80

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319528PMC
November 2012

Integrative subtype discovery in glioblastoma using iCluster.

PLoS One 2012 23;7(4):e35236. Epub 2012 Apr 23.

Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035236PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335101PMC
September 2012

Three-dimensional structures of membrane proteins from genomic sequencing.

Cell 2012 Jun 10;149(7):1607-21. Epub 2012 May 10.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.cell.2012.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641781PMC
June 2012